England's Sistine Chapel lies lost in the western reaches of Gloucestershire. It is smaller, to put it mildly, and older by 350 years. But what it lacks in grandeur it adds in serenity. I would exchange five minutes in the chancel of Kempley church for an hour in Rome. And I would have it to myself.

The church was built by the Normans, with roof timbers ring-dated to 1120, making it one of the earliest surviving roofs in Britain. The nave contains a job lot of admonitory paintings - St Michael with his scales, a Wheel of Life and Damnation over the arch.

The sensation lies in the chancel, composed of the most complete set of Romanesque frescos in northern Europe. Christ sits in the middle of the ceiling on a rainbow, his feet on a globe. He is attended by sun, moon, stars, candelabra, a winged ox and seraphim with books and scrolls, the complete Book of Revelation. Below him sit rows of sepia apostles gazing up at Him from a Romanesque arcade. No inch is left untouched. Here is a bishop, there lay pilgrims heading for a heavenly Jerusalem. Everywhere is chequerboard and zigzag decoration.

The pigments of Kempley chancel are drawn from the earth: reds, whites, ochres and rare imported azurite for blue. The style is that of a culture universal in 12th-century Europe, with a common liturgy, language and artistic style. It might be anywhere from Constantinople to Galicia.

All this arises from my Easter book of the year, Roger Rosewell's Medieval Wall Paintings, a magisterial compendium of this most elusive English vernacular form. It shows how much of this work survives, and in every county in England, some of a quality far exceeding the ghostly fragments that stare out from many church walls.

Wall painting was once the national gallery of England. The imprinting of natural colours into moist plaster defied the passage of time. Kempley's colours seem to glow even more vividly when the walls become moist. Churches were entirely coated in these messages, telling stories, recording pilgrimages, terrifying the wicked, saluting St Christopher, the saint of travellers, or just graffiti celebrating life on Earth.

The Reformation whitewashed over most church murals, or over-painted them with "the word" - biblical texts, creeds and commandments. But substantial sets have come to light, the "Sussex school" at Clayton and Hardham, Copford in Essex, Ickleton in Cambridgeshire and the great Doom painting in St Thomas's, Salisbury. While stained glass, sculpture, screens and icons were stolen and smashed, wall paintings slept undisturbed until roused by scholars such as Ernest Tristram and Clive Rouse.

Many of these paintings would be on London pedestals, had some avaricious director been able to prise them from the walls, as they did so much of the stained glass and statuary now in the V&A and elsewhere. The lovely swaying figures of the Brent Eleigh crucifixion in Suffolk might have stepped from a work by Italian painter Cimabue. Norwich St Gregory's George and Dragon would pass muster in an Italian sanctuary. The terrifying Ladder of Salvation in Chaldon, Surrey, is pure Hieronymus Bosch. The Lily Crucifix in Godshill on the Isle of Wight is delicate beyond compare.

Overwhelming these delights is despair at the sheer ragged incompleteness of it all. To study this elusive art is to gaze on mostly a ruin. It is as if every painting in every gallery were a tattered piece of canvas in a broken frame; as if the parish church as the aesthetic climax of English life, offering a narrative of its past, were just a mausoleum.

This was not always so. The mural tradition dwindled after the Reformation but was brilliantly revived by the Victorians. Richard Gambier-Parry painted the Day of Judgment in his church at Highnam in Gloucestershire, ensuring that his children sat among the saved. George Edmund Street's murals at Garton-in-the-Wolds in Yorkshire were followed by John Loughborough Pearson's at St Augustine, Kilburn, and William Butterfield's at All Saints, Margaret Street, London.

Medieval buildings were revived as they were meant to be, blasts of decoration and colour. To adorn a building was to respect it. Murals covered the walls of Victorian palaces such as the Houses of Parliament, Manchester Town Hall and Cardiff Castle. Everywhere wanted to tell its story. JD Sedding's art nouveau chapel at Llanfair Cilgedin in Gwent has pictures that bring the enveloping hills and trees down into the nave in great sweeps of nature.

The revival was not to last. The Anglican church has always preferred to wrap its proclamation of joy in a cloak of gloom. Walls scraped of limewash by the Victorians have stayed scraped. Most city churches conform to Dickens's dedication to "St Ghastly Grim". Saddest of all, where fragments of medieval mural have been discovered, they are left marooned in surrounding whitewash like so much fruit hurled at the wall.

As I leafed through Rosewell's book I was left baffled by the "eye" of the restorer. It seemed so lacking in self-confidence in refusing to paint areas round the relics and thus restore to them both narrative meaning and some sense of artistic whole. All over England are church walls decorated with dismembered heads, arms, legs, animals, swords on white backgrounds. They are surreal patches, Turner-prize daubs, stripped even of the ghostly antiquity of a crumbling wall for company.

Art conservation must be capable of bringing these walls to life, as Arthur Evans did, however imperfectly, the Minoan murals at Knossos. There are acceptable techniques for reinstating ruined fabric, as there are for damaged painting and woodwork. Few church murals rank as great works of art, and old fragments can be distinguished from new in any imaginative reconstruction.

When the Victorians restored churches such as Stow in Lincolnshire or even Westminster Abbey, they understood that the past of a building can be respected without treating its ruination as somehow hallowed. Modern art has contributed to church tapestry, music and even sculpture. Only murals seem untouchable.

The one medieval church to experience comprehensive reinstatement had to suffer the indignity of first being demolished, and thus released from archaeology's intellectual prison. This is St Teilo's, Swansea, recently moved to Cardiff's St Fagans open-air museum. There, conservators have reinstated what they reasonably assess was its pre-Reformation interior, complete with fittings, a rood screen and murals based on imagined reconstructions.

Everyone should see this building. The colours are brilliant, the reproduction of late-gothic decoration is exact in its scholarship, and the impact is dazzling. The effect is garishly fairground, almost surreal. But the reason St Teilo's is unsettling is not that the murals are untrue to their 15th-century forebears, but that they are true. It is the presiding archaeology of gloom that has made us scared of sometimes seeing the middle ages as they really were. St Teilo's is a comment not just on conservation faddism, but on the education of the modern eye.